Senior army officers "slammed the door" to block a military police investigation into the treatment of prisoners captured after a fierce battle in Iraq, and then tried to deny having done so, a public inquiry into the incident has heard.

Lucy Bowen, a military police special investigations officer, described how commanders of 1 Battalion Princess of Wales Royal Regiment (1PWRR) stopped her from questioning soldiers after the Battle of Danny Boy – Danny Boy was a British checkpoint near Majar al-Kabir, north of Basra – on 14 May 2004, in which at least 20 insurgents were killed and others were wounded and captured.

The inquiry counsel, Jonathan Acton Davis QC, said: "The door was slammed in your face?" Bowen replied: "Yes … they would not allow us to investigate."

Bowen, who was then a captain in the Royal Military Police (RMP), since promoted to major, was giving evidence in London to the al-Sweady inquiry, named after the family of a 19 year-old allegedly killed in the battle.

It was set up after the high court castigated the Ministry of Defence for failing properly to look into allegations that British soldiers had killed unarmed Iraqis and mistreated others.

Responding on Monday to an official MoD document in which Lieutenant Colonel Matthew Maer, commanding officer of 1PWRR, is recorded as saying he and fellow officers themselves asked the military police to investigate the allegations, Bowen told the inquiry that was "absolutely untrue".

She wrote in the margin of a printed copy of an email she received from 1PWRR officers: "Never. He has never made any such request." Maer had described the allegations as "vexatious", according to a document released by the inquiry.

Maer has told the inquiry he was unaware that his officers had failed to co-operate with the military police. He added that he did not recall Bowen "at all".

The inquiry on Monday disclosed a number of exchanges Bowen had with Maer, both via email and verbally, and with his close colleagues. In one, Maer is described as "going nuts" about a report that the military police had invited a judge to make a complaint against his officers.

In one of many attempts to speak to Maer, Bowen was told that he had been angry because she was "interrupting his lunch", the inquiry heard.

She said the second-in-command of the RMP, Colonel Dudley Giles, had later asked her to change a statement she had made previously to the high court about the Danny Boy allegations.

She said she had refused to do so. The high court previously described Giles as an unreliable witness. "It is our view that any court seized of those proceedings should approach his evidence with the greatest caution", the judges said in 2009.

Giles, who has not been called to give evidence to the al-Sweady inquiry, retained his post as deputy provost marshal. He has since retired.

The inquiry heard on Monday that a senior 1PWRR officer, Major (now Colonel) James Coote, had issued an order telling his soldiers to consult his officers before being questioned by the military police. It heard that Coote suggested the soldiers should not be questioned alone. Coote argued in previous evidence to the inquiry that he had given his order out of a duty of care to his soldiers, many of whom were "young men upset by events".

Bowen said on Monday that the military police had inadequate resources in Iraq. They were short of manpower, vehicles and communications – "all of the sort of resources you would need to conduct an investigation", she said.

The inquiry continues, Its chairman, the retired judge Sir Thayne Forbes, is due to complete his report by the end of the year.